Amit Rakhit earns the same salary as other vice presidents leading drug development teams at the Weston-based biotech company Biogen Idec, but, because he is gay, he ends up bringing home about $3,000 less every year. Unlike his married heterosexual co-workers, Rakhit, 42, is taxed on income that goes toward his husband’s health insurance plan; for other spouses, that money is tax-free. Even in states like Massachusetts where gay marriage is legal, same-sex spouses don’t get a tax break from Uncle Sam on medical, dental, and vision insurance because gay marriage isn’t recognized under federal law. Starting Jan. 1, Biogen Idec will begin addressing this inequity, joining just a few dozen companies in the United States that offer a similar type of reimbursement, including three based in Massachusetts. “We cannot let our employees go one more year with this additional burden,” said Javier Barrientos, director of global inclusion at Biogen Idec. “We’re part of the innovation economy, and we’re looking for exceptional talent, and exceptional talent comes in all backgrounds.” Money spent on health care premiums is not considered taxable income, allowing employees to use pretax dollars to buy health insurance. While heterosexual couples get the tax break, same-sex couples do not. To negate the impact, Biogen Idec will add money to affected employees’ paychecks equal to the amount of taxes taken out for their spouses’ benefits — and their children’s, too. This practice, known as grossing up a worker’s pay, will restore an average of $2,000 to $5,000 a year to around 40 of Biogen Idec’s nearly 4,000 US employees, costing the company around $120,000 a year.